1
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Østergaard M, Naver EB, Kaestner A, Willendrup PK, Brüel A, Sørensen HO, Thomsen JS, Schmidt S, Poulsen HF, Theil Kuhn L, Birkedal H. Polychromatic neutron phase-contrast imaging of weakly absorbing samples enabled by phase retrieval. J Appl Crystallogr 2023; 56:673-682. [PMID: 37284268 PMCID: PMC10241042 DOI: 10.1107/s1600576723003011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 04/01/2023] [Indexed: 06/08/2023] Open
Abstract
The use of a phase-retrieval technique for propagation-based phase-contrast neutron imaging with a polychromatic beam is demonstrated. This enables imaging of samples with low absorption contrast and/or improving the signal-to-noise ratio to facilitate e.g. time-resolved measurements. A metal sample, designed to be close to a phase pure object, and a bone sample with canals partially filled with D2O were used for demonstrating the technique. These samples were imaged with a polychromatic neutron beam followed by phase retrieval. For both samples the signal-to-noise ratios were significantly improved and, in the case of the bone sample, the phase retrieval allowed for separation of bone and D2O, which is important for example for in situ flow experiments. The use of deuteration contrast avoids the use of chemical contrast enhancement and makes neutron imaging an interesting complementary method to X-ray imaging of bone.
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Affiliation(s)
- Maja Østergaard
- Department of Chemistry and iNANO, Aarhus University, Gustav Wieds Vej 14, Aarhus, Denmark
| | - Estrid Buhl Naver
- Department of Energy Conversion and Storage, Technical University of Denmark, Fysikvej 310, Kongens Lyngby, Denmark
| | - Anders Kaestner
- Laboratory for Neutron Scattering and Imaging, Paul Scherrer Institute, Villigen, Switzerland
| | - Peter K. Willendrup
- Department of Physics, Technical University of Denmark, Fysikvej 307, Kongens Lyngby, Denmark
- European Spallation Source ERIC, PO Box 176, Lund, Sweden
| | - Annemarie Brüel
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, Aarhus, Denmark
| | - Henning Osholm Sørensen
- Department of Physics, Technical University of Denmark, Fysikvej 307, Kongens Lyngby, Denmark
- Xnovo Technology ApS, Galoche Alle 15, 1, Køge, Denmark
| | | | - Søren Schmidt
- European Spallation Source ERIC, PO Box 176, Lund, Sweden
| | - Henning Friis Poulsen
- Department of Physics, Technical University of Denmark, Fysikvej 307, Kongens Lyngby, Denmark
| | - Luise Theil Kuhn
- Department of Energy Conversion and Storage, Technical University of Denmark, Fysikvej 310, Kongens Lyngby, Denmark
| | - Henrik Birkedal
- Department of Chemistry and iNANO, Aarhus University, Gustav Wieds Vej 14, Aarhus, Denmark
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2
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Kutsal M, Poulsen HF, Winther G, Sørensen HO, Detlefs C. High-resolution 3D X-ray diffraction microscopy: 3D mapping of deformed metal microstructures. J Appl Crystallogr 2022; 55:1125-1138. [PMID: 36249499 PMCID: PMC9533755 DOI: 10.1107/s1600576722007361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 07/18/2022] [Indexed: 11/22/2022] Open
Abstract
A full-field X-ray diffraction contrast method is presented (high-resolution 3D X-ray diffraction), for 3D mapping of plastically deformed microstructures. The essence of the method is the introduction of a 2D detector in the optical mid-field regime. The properties and limitations of the method are estimated by numerical simulations. Three-dimensional X-ray diffraction microscopy, 3DXRD, has become an established tool for orientation and strain mapping of bulk polycrystals. However, it is limited to a finite spatial resolution of ∼1.5–3 µm. Presented here is a high-resolution modality of the technique, HR-3DXRD, for 3D mapping of submicrometre-sized crystallites or subgrains with high spatial and angular resolution. Specifically, the method is targeted to visualization of metal microstructures at industrially relevant degrees of plastic deformation. Exploiting intrinsic crystallographic properties of such microstructures, the high resolution is obtained by placing a high-resolution imaging detector in between the near-field and far-field regimes. This configuration enables 3D mapping of deformation microstructure by determining the centre of mass and volume of the subgrains and generating maps by tessellation. The setup is presented, together with a data analysis approach. Full-scale simulations are used to determine limitations and to demonstrate HR-3DXRD on realistic phantoms. Misalignments in the setup are shown to cause negligible shifts in the position and orientation of the subgrains. Decreasing the signal-to-noise ratio is observed to lead primarily to a loss in the number of determined diffraction spots. Simulations of an α-Fe sample deformed to a strain of εvM = 0.3 and comprising 828 subgrains show that, despite the high degree of local texture, 772 of the subgrains are retrieved with a spatial accuracy of 0.1 µm and an orientation accuracy of 0.0005°.
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3
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Rasmussen PW, Sørensen HO, Bruns S, Dahl AB, Christensen AN. Improved dynamic imaging of multiphase flow by constrained tomographic reconstruction. Sci Rep 2021; 11:12501. [PMID: 34127711 PMCID: PMC8203785 DOI: 10.1038/s41598-021-91776-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/31/2021] [Indexed: 11/09/2022] Open
Abstract
Dynamic tomography has become an important technique to study fluid flow processes in porous media. The use of laboratory X-ray tomography instruments is, however, limited by their low X-ray brilliance. The prolonged exposure times, in turn, greatly limit temporal resolution. We have developed a tomographic reconstruction algorithm that maintains high image quality, despite reducing the exposure time and the number of projections significantly. Our approach, based on the Simultaneous Iterative Reconstruction Technique, mitigates the problem of few and noisy exposures by utilising a high-quality scan of the system before the dynamic process is started. We use the high-quality scan to initialise the first time step of the dynamic reconstruction. We further constrain regions of the dynamic reconstruction with a segmentation of the static system. We test the performance of the algorithm by reconstructing the dynamics of fluid separation in a multiphase system. The algorithm is compared quantitatively and qualitatively with several other reconstruction algorithms and we show that it can maintain high image quality using only a fraction of the normally required number of projections and with a substantially larger noise level. By robustly allowing fewer projections and shorter exposure, our algorithm enables the study of faster flow processes using laboratory tomography instrumentation but it can also be used to improve the reconstruction quality of dynamic synchrotron experiments.
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Affiliation(s)
- Peter Winkel Rasmussen
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.
| | | | - Stefan Bruns
- Helmholtz-Zentrum Hereon, Institute for Metallic Biomaterials, 21502, Geesthacht, Germany
| | - Anders Bjorholm Dahl
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Anders Nymark Christensen
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.
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4
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Chavez Panduro EA, Cordonnier B, Gawel K, Børve I, Iyer J, Carroll SA, Michels L, Rogowska M, McBeck JA, Sørensen HO, Walsh SDC, Renard F, Gibaud A, Torsæter M, Breiby DW. Real Time 3D Observations of Portland Cement Carbonation at CO 2 Storage Conditions. Environ Sci Technol 2020; 54:8323-8332. [PMID: 32525672 PMCID: PMC7467647 DOI: 10.1021/acs.est.0c00578] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 06/06/2020] [Accepted: 06/11/2020] [Indexed: 06/11/2023]
Abstract
Depleted oil reservoirs are considered a viable solution to the global challenge of CO2 storage. A key concern is whether the wells can be suitably sealed with cement to hinder the escape of CO2. Under reservoir conditions, CO2 is in its supercritical state, and the high pressures and temperatures involved make real-time microscopic observations of cement degradation experimentally challenging. Here, we present an in situ 3D dynamic X-ray micro computed tomography (μ-CT) study of well cement carbonation at realistic reservoir stress, pore-pressure, and temperature conditions. The high-resolution time-lapse 3D images allow monitoring the progress of reaction fronts in Portland cement, including density changes, sample deformation, and mineral precipitation and dissolution. By switching between flow and nonflow conditions of CO2-saturated water through cement, we were able to delineate regimes dominated by calcium carbonate precipitation and dissolution. For the first time, we demonstrate experimentally the impact of the flow history on CO2 leakage risk for cement plugging. In-situ μ-CT experiments combined with geochemical modeling provide unique insight into the interactions between CO2 and cement, potentially helping in assessing the risks of CO2 storage in geological reservoirs.
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Affiliation(s)
- Elvia A. Chavez Panduro
- Department
of Physics, Norwegian University of Science
and Technology (NTNU), Høgskoleringen 5, 7491 Trondheim, Norway
- SINTEF
Energy Research, Postboks
4761 Torgarden, 7465, Trondheim, Norway
| | - Benoît Cordonnier
- The
Njord Centre, Department of Geosciences, University of Oslo, Oslo, 0315, Norway
- ESRF,
European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Kamila Gawel
- SINTEF
Industry, S. P. Andersens veg 15B, 7031 Trondheim, Norway
| | - Ingrid Børve
- Department
of Physics, Norwegian University of Science
and Technology (NTNU), Høgskoleringen 5, 7491 Trondheim, Norway
| | - Jaisree Iyer
- Atmospheric
Earth and Energy Division, Lawrence Livermore
National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Susan A. Carroll
- Atmospheric
Earth and Energy Division, Lawrence Livermore
National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Leander Michels
- Department
of Physics, Norwegian University of Science
and Technology (NTNU), Høgskoleringen 5, 7491 Trondheim, Norway
| | - Melania Rogowska
- Department
of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark
| | - Jessica Ann McBeck
- The
Njord Centre, Department of Geosciences, University of Oslo, Oslo, 0315, Norway
| | - Henning Osholm Sørensen
- Department
of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark
- Department
of Physics, Technical University of Denmark, Fysikvej, 2800 Kongens Lyngby, Denmark
| | - Stuart D. C. Walsh
- Resources
Engineering, Monash University, Melbourne, VIC 3800, Australia
| | - François Renard
- The
Njord Centre, Department of Geosciences, University of Oslo, Oslo, 0315, Norway
- University
Grenoble Alpes, University Savoie Mont Blanc,
CNRS, IRD, IFSTTAR, ISTerre, 38000, Grenoble, France
| | - Alain Gibaud
- LUNAM,
IMMM, UMR 6283 CNRS, Le Mans Université, 72085 Le Mans Cedex
09, France
| | - Malin Torsæter
- SINTEF
Industry, S. P. Andersens veg 15B, 7031 Trondheim, Norway
| | - Dag W. Breiby
- PoreLab,
Department of Physics, Norwegian University
of Science and Technology (NTNU), Høgskoleringen 5, 7491 Trondheim, Norway
- Department
of Microsystems, University of South-Eastern
Norway, Campus Bakkenteigen, 3184 Borre, Norway
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5
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Ögren M, Jha D, Dobberschütz S, Müter D, Carlsson M, Gulliksson M, Stipp SLS, Sørensen HO. Numerical simulations of NMR relaxation in chalk using local Robin boundary conditions. J Magn Reson 2019; 308:106597. [PMID: 31546178 DOI: 10.1016/j.jmr.2019.106597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 09/11/2019] [Accepted: 09/12/2019] [Indexed: 06/10/2023]
Abstract
The interpretation of nuclear magnetic resonance (NMR) data is of interest in a number of fields. In Ögren (2014) local boundary conditions for random walk simulations of NMR relaxation in digital domains were presented. Here, we have applied those boundary conditions to large, three-dimensional (3D) porous media samples. We compared the random walk results with known solutions and then applied them to highly structured 3D domains, from images derived using synchrotron radiation CT scanning of North Sea chalk samples. As expected, there were systematic errors caused by digitalization of the pore surfaces so we quantified those errors, and by using linear local boundary conditions, we were able to significantly improve the output. We also present a technique for treating numerical data prior to input into the ESPRIT algorithm for retrieving Laplace components of time series from NMR data (commonly called T-inversion).
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Affiliation(s)
- M Ögren
- Nano-Science Center, Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 København Ø, Denmark; School of Science and Technology, Örebro University, 701 82 Örebro, Sweden.
| | - D Jha
- Nano-Science Center, Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 København Ø, Denmark
| | - S Dobberschütz
- Nano-Science Center, Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 København Ø, Denmark
| | - D Müter
- Nano-Science Center, Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 København Ø, Denmark
| | - M Carlsson
- Center for Mathematical Sciences, Lund University, Box 118, 22100 Lund, Sweden
| | - M Gulliksson
- School of Science and Technology, Örebro University, 701 82 Örebro, Sweden
| | - S L S Stipp
- Nano-Science Center, Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 København Ø, Denmark
| | - H O Sørensen
- Nano-Science Center, Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 København Ø, Denmark
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6
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Stie MB, Jones M, Sørensen HO, Jacobsen J, Chronakis IS, Nielsen HM. Acids ‘generally recognized as safe’ affect morphology and biocompatibility of electrospun chitosan/polyethylene oxide nanofibers. Carbohydr Polym 2019; 215:253-262. [DOI: 10.1016/j.carbpol.2019.03.061] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 02/22/2019] [Accepted: 03/17/2019] [Indexed: 11/25/2022]
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7
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Wittig NK, Laugesen M, Birkbak ME, Bach-Gansmo FL, Pacureanu A, Bruns S, Wendelboe MH, Brüel A, Sørensen HO, Thomsen JS, Birkedal H. Canalicular Junctions in the Osteocyte Lacuno-Canalicular Network of Cortical Bone. ACS Nano 2019; 13:6421-6430. [PMID: 31095362 DOI: 10.1021/acsnano.8b08478] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The osteocyte lacuno-canalicular network (LCN) is essential for bone remodeling because osteocytes regulate cell recruitment. This has been proposed to occur through liquid-flow-induced shear forces in the canaliculi. Models of the LCN have thus far assumed that it contains canaliculi connecting the osteocyte lacunae. However, here, we reveal that enlarged spaces occur at places where several canaliculi cross; we name these spaces canalicular junctions. We characterize them in detail within mice cortical bone using synchrotron nanotomography at two length scales, with 50 and 130 nm voxel size, and show that canalicular junctions occur at a density similar to that of osteocyte lacunae and that canalicular junctions tend to cluster. Through confocal laser scanning microscopy, we show that canalicular junctions are widespread as we have observed them in cortical bone from several species, even though the number density of the canalicular junctions was not universal. Fluid flow simulations of a simple model system with and without a canalicular junction clearly show that liquid mass transport and flow velocities are altered by the presence of canalicular junctions. We suggest that these canalicular junctions may play an important role in osteocyte communication and possibly also in canalicular fluid flow. Therefore, we believe that they constitute an important component in the bone osteocyte network.
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Affiliation(s)
| | | | | | | | | | - Stefan Bruns
- Department of Chemistry, University of Copenhagen , 2100 Copenhagen Ø , Denmark
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8
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Yousefi N, Wong KKW, Hosseinidoust Z, Sørensen HO, Bruns S, Zheng Y, Tufenkji N. Hierarchically porous, ultra-strong reduced graphene oxide-cellulose nanocrystal sponges for exceptional adsorption of water contaminants. Nanoscale 2018; 10:7171-7184. [PMID: 29620092 DOI: 10.1039/c7nr09037d] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Self-assembly of graphene oxide (GO) nanosheets into porous 3D sponges is a promising approach to exploit their capacity to adsorb contaminants while facilitating the recovery of the nanosheets from treated water. Yet, forming mechanically robust sponges with suitable adsorption properties presents a significant challenge. Ultra-strong and highly porous 3D sponges are formed using GO, vitamin C (VC), and cellulose nanocrystals (CNCs) - natural nanorods isolated from wood pulp. CNCs provide a robust scaffold for the partially reduced GO (rGO) nanosheets resulting in an exceptionally stiff nanohybrid. The concentration of VC as a reducing agent plays a critical role in tailoring the pore architecture of the sponges. By using excess amounts of VC, a unique hierarchical pore structure is achieved, where VC grains act as soft templates for forming millimeter-sized pores, the walls of which are also porous and comprised of micron-sized pores. The unique hierarchical pore structure ensures the interconnectivity of pores even at the core of large sponges as evidenced by micro and nano X-ray computed tomography. The unique pore architecture translates into an exceptional specific surface area for adsorption of a wide range of contaminants, such as dyes, heavy metals, pharmaceuticals and cyanotoxin from water.
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Affiliation(s)
- Nariman Yousefi
- Department of Chemical Engineering, McGill University, Montreal, QC, Canada.
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9
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Chavez Panduro EA, Torsæter M, Gawel K, Bjørge R, Gibaud A, Yang Y, Bruns S, Zheng Y, Sørensen HO, Breiby DW. In-Situ X-ray Tomography Study of Cement Exposed to CO 2 Saturated Brine. Environ Sci Technol 2017; 51:9344-9351. [PMID: 28701043 DOI: 10.1021/acs.est.6b06534] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
For successful CO2 storage in underground reservoirs, the potential problem of CO2 leakage needs to be addressed. A profoundly improved understanding of the behavior of fractured cement under realistic subsurface conditions including elevated temperature, high pressure and the presence of CO2 saturated brine is required. Here, we report in situ X-ray micro computed tomography (μ-CT) studies visualizing the microstructural changes upon exposure of cured Portland cement with an artificially engineered leakage path (cavity) to CO2 saturated brine at high pressure. Carbonation of the bulk cement, self-healing of the leakage path in the cement specimen, and leaching of CaCO3 were thus directly observed. The precipitation of CaCO3, which is of key importance as a possible healing mechanism of fractured cement, was found to be enhanced in confined regions having limited access to CO2. For the first time, the growth kinetics of CaCO3 under more realistic well conditions have thus been estimated quantitatively. Combining the μ-CT observations with scanning electron microscopy resulted in a detailed understanding of the processes involved in the carbonation of cement.
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Affiliation(s)
- E A Chavez Panduro
- Department of Physics, Norwegian University of Science and Technology , Høgskoleringen 5, 7491 Trondheim, Norway
| | - M Torsæter
- SINTEF Petroleum Research , Trondheim, Norway
| | - K Gawel
- SINTEF Petroleum Research , Trondheim, Norway
| | - R Bjørge
- SINTEF Materials and Chemistry , Trondheim, Norway
| | - A Gibaud
- LUMAN, IMMM, UMR 6283 CNRS, Université du Maine , Le Mans Cedex 09, France
| | - Y Yang
- Nano-Science Center, Department of Chemistry, University of Copenhagen , DK-2100 Copenhagen, Denmark
| | - S Bruns
- Nano-Science Center, Department of Chemistry, University of Copenhagen , DK-2100 Copenhagen, Denmark
| | - Y Zheng
- Department of Physics, Technical University of Denmark , Lyngby, Denmark
| | - H O Sørensen
- Nano-Science Center, Department of Chemistry, University of Copenhagen , DK-2100 Copenhagen, Denmark
| | - D W Breiby
- Department of Physics, Norwegian University of Science and Technology , Høgskoleringen 5, 7491 Trondheim, Norway
- Department of Microsystems, University College of Southeast Norway , Campus Vestfold, 3184 Borre, Norway
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10
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Müter D, Sørensen HO, Oddershede J, Dalby KN, Stipp SLS. Microstructure and micromechanics of the heart urchin test from X-ray tomography. Acta Biomater 2015; 23:21-26. [PMID: 25983316 DOI: 10.1016/j.actbio.2015.05.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 05/04/2015] [Accepted: 05/10/2015] [Indexed: 11/17/2022]
Abstract
The microstructure of many echinoid species has long fascinated scientists because of its high porosity and outstanding mechanical properties. We have used X-ray microtomography to examine the test of Echinocardium cordatum (heart urchin), a burrowing cousin of the more commonly known sea urchins. Three dimensional imaging demonstrates that the bulk of the test is composed of only two distinct, highly porous, fenestrated regions (stereom), in which the thickness of the struts is constant. Different degrees of porosity are achieved by varying the spacing of the struts. Drawing an analogy to vertebrate trabecular bone, where for example, human bone has a connectivity density of ≈1/mm(3), we measure up to 150,000 strut connections per mm(3). Simulations of mechanical loading using finite element calculations indicate that the test performs at very close to the optimum expected for foams, highlighting the functional link between structure and mechanical properties.
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Affiliation(s)
- D Müter
- Nano-Science Center, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - H O Sørensen
- Nano-Science Center, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - J Oddershede
- Department of Physics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - K N Dalby
- Nano-Science Center, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - S L S Stipp
- Nano-Science Center, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
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11
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Nielsen CBO, Sørensen HO, Kongsted J. Comparison between Theoretically and Experimentally Determined Electronic Properties: Applications to Two-Photon Singlet Oxygen Sensitizers. J Phys Chem A 2015; 119:1906-16. [DOI: 10.1021/jp5122849] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Christian Benedikt Orea Nielsen
- Polymer
Department, Risø National Laboratory, Frederiksborgvej 399, DK-4000 Roskilde, Denmark
- Department
of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Henning Osholm Sørensen
- Nano-Science
Center, Department of Chemistry, University of Copenhagen, Universitetsparken
5, DK-2100 Copenhagen
Ø, Denmark
| | - Jacob Kongsted
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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12
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Christiansen BC, Dideriksen K, Katz A, Nedel S, Bovet N, Sørensen HO, Frandsen C, Gundlach C, Andersson MP, Stipp SLS. Incorporation of monovalent cations in sulfate green rust. Inorg Chem 2014; 53:8887-94. [PMID: 25144528 DOI: 10.1021/ic500495a] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Green rust is a naturally occurring layered mixed-valent ferrous-ferric hydroxide, which can react with a range of redox-active compounds. Sulfate-bearing green rust is generally thought to have interlayers composed of sulfate and water. Here, we provide evidence that the interlayers also contain monovalent cations, using X-ray photoelectron spectroscopy and synchrotron X-ray scattering. For material synthesized with Na(+), K(+), Rb(+), or Cs(+), interlayer thickness derived from basal plane spacings correlates with the radius of the monovalent cation. In addition, sequential washing of the materials with water showed that Na(+) and K(+) were structurally fixed in the interlayer, whereas Rb(+) and Cs(+) could be removed, resulting in a decrease in the basal layer spacing. The incorporation of cations in the interlayer opens up new possibilities for the use of sulfate green rust for exchange reactions with both anions and cations: e.g., radioactive Cs.
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Affiliation(s)
- B C Christiansen
- Nano-Science Center, Department of Chemistry, University of Copenhagen , Universitetsparken 5, 2100 Copenhagen, Denmark
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13
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Straasø T, Müter D, Sørensen HO, Als-Nielsen J. Objective algorithm to separate signal from noise in a Poisson-distributed pixel data set. J Appl Crystallogr 2013. [DOI: 10.1107/s0021889813006511] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
A statistical method to determine the background level and separate signal from background in a Poisson-distributed background data set is described. The algorithm eliminates the pixel with the highest intensity value in an iterative manner until the sample variance equals the sample mean within the estimated uncertainties. The eliminated pixels then contain signal superimposed on the background, so the integrated signal can be obtained by summation or by a simple extension by profile fitting depending on the user's preferences. Two additional steps remove `outliers' and correct for the underestimated extension of the peak area, respectively. The algorithm can be easily modified to specific needs, and an application on crystal truncation rods is presented, dealing with a sloping background.
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14
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Oddershede J, Schmidt S, Poulsen HF, Sørensen HO, Wright J, Reimers W. Determining grain resolved stresses in polycrystalline materials using three-dimensional X-ray diffraction. J Appl Crystallogr 2010. [DOI: 10.1107/s0021889810012963] [Citation(s) in RCA: 147] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
An algorithm is presented for characterization of the grain resolved (type II) stress states in a polycrystalline sample based on monochromatic X-ray diffraction data. The algorithm is a robust 12-parameter-per-grain fit of the centre-of-mass grain positions, orientations and stress tensors including error estimation and outlier rejection. The algorithm is validated by simulations and by two experiments on interstitial free steel. In the first experiment, using only a far-field detector and a rotation range of 2 × 110°, 96 grains in one layer were monitored during elastic loading and unloading. Very consistent results were obtained, with mean resolutions for each grain of approximately 10 µm in position, 0.05° in orientation, and 8, 20 and 13 × 10−5in the axial, normal and shear components of the strain, respectively. The corresponding mean deviations in stress are 30, 50 and 15 MPa in the axial, normal and shear components, respectively, though some grains may have larger errors. In the second experiment, where a near-field detector was added, ∼2000 grains were characterized with a positional accuracy of 3 µm.
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Sørensen HO, Stuhr-Hansen N. 4-Bromoselenoanisole. Acta Crystallogr Sect E Struct Rep Online 2009; 65:o1665-6. [PMID: 21582926 PMCID: PMC2969389 DOI: 10.1107/s160053680902296x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2009] [Accepted: 06/15/2009] [Indexed: 11/10/2022]
Abstract
The title compound, 1-bromo-4-methylselenobenzene, C7H7BrSe, was prepared by methylation of 4-bromoselenophenolate with methyl iodide, and crystals suitable for structure determination were obtained by sublimation. The molecule is essentially planar; the Se—Me bond is rotated by only 2.59 (19)° out of the least-squares plane of the benzene ring. The most pronounced intermolecular interactions are two hydrogen bonds of the type C—H⋯π, which determine a herring-bone pattern in the crystal packing.
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Sørensen HO, Stuhr-Hansen N. 1,4-Bis(4-chlorophenylseleno)-2,5-dimethoxybenzene. Acta Crystallogr Sect E Struct Rep Online 2009; 65:o13. [PMID: 21581591 PMCID: PMC2967934 DOI: 10.1107/s1600536808039469] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2008] [Accepted: 11/24/2008] [Indexed: 11/28/2022]
Abstract
The title compound, C20H16Cl2O2Se2, utilizes the symmetry of the crystallographic inversion center. Molecular chains are formed through symmetric C—H⋯Cl interactions around inversion centers, mimicking the commonly observed symmetric hydrogen-bonded dimer pattern often found in carboxylic acids.
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Stuhr-Hansen N, Götze TF, Henriksen L, Sølling TI, Langkilde A, Sørensen HO. Sparing the ortho-position in nucleophilic aromatic substitution-specific displacement of the 4-SePh group in 2,4-bis(phenylseleno)nitrobenzene. Heteroatom Chem 2009. [DOI: 10.1002/hc.20519] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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18
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Gumm A, Hammershøi A, Kofod-Hansen M, Mønsted O, Osholm Sørensen H. First aminoacetone chelate: [Co(tren){NH2CH2C(O)CH3}]3+-a substrate binding and activation model for zinc(II)-dependent 5-aminolaevulinic acid dehydratase. Dalton Trans 2007:3227-31. [PMID: 17893767 DOI: 10.1039/b707186h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The complex p-[Co(tren){NH(2)CH(2)C(O)CH(3)}](ClO(4))(3).H(2)O was produced stereoselectively from [Co(tren)(O(3)SCF(3))(2)]O(3)SCF(3) () and 2-(aminomethyl)-2-methyl-1,3-dioxolane. The structure of was determined by X-ray crystallography. The complex is the first aminoacetone chelate to be reported and the first structurally characterized example of a non-conjugated ketone moiety coordinated to cobalt(iii). The robust complex was stable to aquation in strong acid and behaved as an acid with pK(a) = 4.99(1) indicative of a strong activation of the aminoacetone ligand towards deprotonation. The complex constitutes a structural model for a proposed substrate binding mode relevant for substrate activation of the zinc(ii)-dependent enzyme 5-aminolaevulinic acid dehydratase.
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Affiliation(s)
- Andreas Gumm
- Department of Chemistry, University of Copenhagen, DK-2100, Copenhagen Ø, Denmark
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Abildgaard J, Hansen PE, Josephsen J, Hansen BK, Sørensen HO, Larsen S. Synthesis and characterization of nickel-, palladium- and platinum(II) complexes of three o,o′-dihydroxydiarylazo dyes: Determination of the coordination geometry of this comprehensive series of tridentate diaryl dye complexes by combining results from NMR and X-ray experiments with theoretical ab initio calculations. Inorganica Chim Acta 2006. [DOI: 10.1016/j.ica.2006.05.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Sørensen HO, Magnussen M, Stuhr-Hansen N. ( E, E, E)-1,3,5-Tris[4-(acetylsulfanyl)styryl]benzene toluene hemisolvate. Acta Crystallogr C 2005; 61:o503-5. [PMID: 16082101 DOI: 10.1107/s0108270105020949] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2005] [Accepted: 06/30/2005] [Indexed: 11/11/2022] Open
Abstract
The first crystal structure of a three-terminal sulfur end-capped oligophenylenevinylene, C36H30O3S3 x 0.5C7H8, has been determined at 122 (1) K. The molecular threefold symmetry is not utilized in the crystal structure. It is confirmed that the double bonds have been fully transformed into a trans configuration by iodine treatment.
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Affiliation(s)
- Henning Osholm Sørensen
- Centre for Crystallographic Studies, Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark.
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Rae AD, Mossin S, Sørensen HO. Structure refinement of a twinned pseudo-symmetric crystal of [Mn(C10H24N4)(NCO)2]+*ClO4-. Acta Crystallogr B 2005; 61:407-17. [PMID: 16041090 DOI: 10.1107/s0108768105015211] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2005] [Accepted: 05/12/2005] [Indexed: 11/10/2022]
Abstract
The crystal studied is a 0.545 (1):0.455 twin, space group C\bar 1, Z = 16, and is a commensurate occupational and displacive modulation of a Z = 4 idealized parent structure with the space group A2/a and a(p) = a/2, b(p) = b/2, c(p) = c. A hierarchical approach to solution and refinement led sequentially to structures in the space groups A2/a, P2(1)/n, P\bar 1 and finally C\bar 1. The major and minor components of the reflection intensities could be identified using irreducible representations of A2/a and P2(1)/n, which in turn suggested suitable constraints and restraints for optimizing the refinement pathway. Comparative refinement was used to show the correctness of the final structure solution and how appropriately chosen constrained refinement allowed an escape from a false minima.
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Affiliation(s)
- Alan David Rae
- Research School of Chemistry, The Australian National University, Canberra ACT 0200, Australia.
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Birk T, Sørensen HO, Bendix J. Two square-pyramidal chromium(V)–nitride complexes: bis(2-methylquinolin-8-olato)nitridochromium(V) and nitridobis(2-sulfidopyridine N-oxide)chromium(V). Acta Crystallogr C 2005; 61:m231-3. [PMID: 15876706 DOI: 10.1107/s0108270105008693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2005] [Accepted: 03/17/2005] [Indexed: 11/10/2022] Open
Abstract
Two new chromium(V)-nitride complexes with a coordination sphere completed by bidentate ligands have been synthesized and structurally characterized. Bis(2-methylquinolin-8-olato)nitridochromium(V), [Cr(C10H8NO)2(N)], has the coordination sphere completed by an equatorial N2O2 set of ligators. The compound crystallizes with the five-coordinate complexes at sites with twofold rotational symmetry and all Cr-N bond directions aligned with the crystallographic b axis. Nitridobis(2-sulfidopyridine N-oxide)chromium(V), [Cr(C5H4NOS)2(N)], crystallizes with the molecules on general positions and has an equatorial S2O2 coordination environment, which is unprecedented among nitride complexes of the first-row transition metals. In both systems, Cr[triple-bond]N bonds are short at ca 1.56 A.
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Affiliation(s)
- Torben Birk
- Inorganic Chemistry, Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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Mossin S, Sørensen HO, Weihe H, Glerup J, Søtofte I. Manganese (III) cyclam complexes with aqua, iodo, nitrito, perchlorato and acetic acid/acetato axial ligands. Inorganica Chim Acta 2005. [DOI: 10.1016/j.ica.2004.10.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Barfod R, Eriksen J, Golding BT, Hammershøi A, Jacobsen TA, Langkilde A, Larsen S, Mønsted O, Sargeson AM, Sørensen HO. Facile cobalt(iii) template synthesis of novel branched hexadentate polyamine monocarboxylates. Dalton Trans 2005:491-500. [PMID: 15672193 DOI: 10.1039/b416994h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
New hexadentate polyamine monocarboxylate ligands, 11-amino-9-(2-aminoethyl)-3,6,9-triazaundecanoate (tren-engly-), 12-amino-10-(2-aminoethyl)-3,7,10-triazadodecanoate (tren-tngly-) and 13-amino-11-(2-aminoethyl)-3,8,11-triazatridecanoate (tren-bngly-), were synthesized by intramolecular coupling of tetradentate tris(2-aminoethyl)amine (tren) and didentate N-([small omega]-formylalkyl)glycinates, OCH(CH2)nNHCH2CO2-, in easily and stereoselectively assembled cobalt(III) templates, p-[Co(tren){(RO)2CH(CH2)nNHCH2CO2}](O3SCF3)2, n = 1-3 (R = Me or Et). The reaction sequences comprised assembly of the template from [Co(tren)(O3SCF3)2]O3SCF3 (1) and (RO)2CH(CH2)nNHCH2CO2Et, deprotection of the pendant acetal in acid, intramolecular condensation of the resulting aldehyde with a coordinated primary amine at intermediate pH to form the imine and reduction of this by NaBH4. For n= 1, imine formation occurred exclusively at the primary amine trans to the carboxylate producing the hexadentate 11-amino-9-(2-aminoethyl)-3,6,9-triazaundeca-5-enoato (tren-enimgly-) complex, i-[Co(tren-enimgly)]Cl2.3.5H2O. In all instances, subsequent imine reduction gave the s isomer complex, exclusively. Complexes p-[Co(tren){(MeO)2CHCH2gly}](O3SCF3)2 (3), i-[Co(tren-enimgly)]ZnCl4.H2O (5), s-[Co(tren-engly)]ZnCl(4)(s-6), s-[Co(tren-tngly)]ZnCl4.H2O (s-7) and s-[Co(tren-bngly)ZnCl3]2ZnCl4 (s-8) were structurally characterized by X-ray crystallography. Charcoal-catalyzed equilibration of s-[Co(tren-engly)]Cl(2).2H(2)O dissolved in water produced the s- (s-6), p- (p-6) and t-[Co(tren-engly)]2+ (t-6) isomers in comparable amounts. p-6 and t-6 were also structurally characterized as their tetrachlorozincate and chloride salts, respectively. In base-catalyzed reactions, s-6 and t-6 each also formed p-6. Reduction of s-[Co(tren-engly)]Cl2.2H2O with (NH4)2S and acidification liberated the pentaamino carboxylic acid ligand which was isolated as the hydrochloride salt.
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Affiliation(s)
- Rasmus Barfod
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen O, Denmark
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Madsen AØ, Sørensen HO, Flensburg C, Stewart RF, Larsen S. Modeling of the nuclear parameters for H atoms in X-ray charge-density studies. Acta Crystallogr A 2004; 60:550-61. [PMID: 15507737 DOI: 10.1107/s0108767304018306] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2004] [Accepted: 07/26/2004] [Indexed: 11/10/2022] Open
Abstract
Extensive and precise X-ray diffraction data for xylitol have been used to test different approaches to estimate nuclear parameters for H atoms in charge-density studies. The parameters from a neutron diffraction study of the same compound were taken as a reference. The resulting static charge densities obtained for the different approaches based on a multipole model were subjected to a topological analysis. The comparative analysis led to the following results. The procedure of extending the X-H bond to match bond lengths from neutron diffraction studies provides the best agreement with the neutron positional parameters. An isotropic model for the atomic displacements of H atoms is highly unsatisfactory and leads to significant deviations for the properties of the bond critical points including those that only involve non-H atoms. Anisotropic displacement parameters for H atoms can be derived from the X-ray data that are in agreement with the values from the neutron study, and the resulting charge-density models are in good agreement with the reference model. The anisotropic displacement parameters for H atoms are derived from the X-ray data as a sum of the external (rigid-body) and internal vibrations. The external vibrations are obtained from a TLS analysis of the ADPs of the non-H atoms and the internal vibrations from analysis of neutron diffraction studies of related compounds. The results from the analysis of positional and thermal parameters were combined to devise a 'best anisotropic' model, which was employed for three other systems where X-ray and neutron data were available. The results from the topological analysis of these systems confirm the success of the 'best anisotropic' model in providing parameters for the H atoms that give charge densities in agreement with the reference models based on H-atom parameters derived from neutron diffraction.
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Affiliation(s)
- Anders Østergaard Madsen
- Centre for Crystallographic Studies, Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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Abstract
Violations of the systematically absent reflections in a data set of stibnite in the space groupPnmahave been shown to originate from multiple diffraction, and for a few reflections additional intensity from λ/2 radiation was found. The study was performed by measurements of the Ψ profiles for a number of reflections and comparison with the theoretical Ψ profiles.
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Mossin S, Weihe H, Sørensen HO, Lima N, Sessoli R. Rationalisation of weak ferromagnetism in manganese(iii) chains: the relation between structure and ordering phenomena. Dalton Trans 2004:632-9. [PMID: 15252527 DOI: 10.1039/b314355d] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis, structure and magnetic properties of the one-dimensional chain compounds [Mn(cyclam)(SO4)]ClO4.H2O (1) and [Mn(cyclam)(HCOO)](CF3SO3)(ClO4) (2) are reported. Cyclam is the cyclic tetradentate ligand 1,4,7,11-tetraazacyclotetradecane. Both chain compounds exhibit antiferromagnetic interactions within the chains. A magnetic ordering phase transition at 5.5 K in (1) is investigated by magnetisation measurements along the three principal crystallographic axes of a single crystal and the results show unambiguously that the ferromagnetic ordering is only taking place along one crystallographic axis. The spin structure of the magnetic ordered phase and the magnitude of the ferromagnetic moment are correlated with the crystal structure and symmetry of the compound.
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Affiliation(s)
- Susanne Mossin
- Department of Chemistry, University of Copenhagen, Denmark
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Sørensen HO, Stewart RF, McIntyre GJ, Larsen S. Simultaneous variation of multipole parameters and Gram-Charlier coefficients in a charge-density study of tetrafluoroterephthalonitrile based on X-ray and neutron data. Acta Crystallogr A 2003; 59:540-50. [PMID: 14581753 DOI: 10.1107/s0108767303018713] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2003] [Accepted: 08/22/2003] [Indexed: 11/10/2022] Open
Abstract
Difficulties encountered in modelling the scattering of fluorine in organic compounds have been investigated through refinements of accurate X-ray and neutron diffraction data measured on tetrafluoroterephthalonitrile, TFT, at 122.4 K. Multipole refinements led to a highly contracted octopole on fluorine. The subsequent analysis revealed that fluorine does not possess a valence octopole but exhibits anharmonic thermal motion that can be modelled by the octopole multipole parameters. The scattering contribution from the octopole shows the same cubic dependence in the scattering vector as the Gram-Charlier expansion of the nuclear displacements to third order. The analysis also showed that refinement of third-order Gram-Charlier coefficients on fluorine requires data to at least 0.93 A(-1) resolution in sinthetas/lambda. The X-ray data extending to 1.27 A(-1) were of sufficient resolution to include third-order Gram-Charlier coefficients for N, F and the cyano C atoms in the refinement, whereas the neutron data only enabled refinement of the third-order Gram-Charlier coefficients for nitrogen. The refinements of the neutron and X-ray diffraction data yielded identical atomic displacement parameters for all the atoms. Though inclusion of anharmonic motion for N and F atoms provides the best model, it does not affect the crystal electron density, and all intramolecular bond critical points have identical features. Application of the anharmonic model, however, leads to small differences in the intermolecular interactions, which is illustrated by the electrostatic potential adjacent to the N atom. The characteristics of the C-F bond were elucidated by the topological analysis of the crystal electron density, which also supported the proposed quinonoid structure of the benzene ring.
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Affiliation(s)
- Henning Osholm Sørensen
- Centre for Crystallographic Studies, Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
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Sørensen HO, Larsen S. Measurement of high-quality diffraction data with a Nonius KappaCCD diffractometer: finding the optimal experimental parameters. J Appl Crystallogr 2003. [DOI: 10.1107/s0021889803008434] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The influence of the different experimental parameters on the quality of the diffraction data collected on tetrafluoroterephthalonitrile (TFT) with a Nonius KappaCCD instrument has been examined. Data sets measured with different scan widths (0.25°, 0.50°, 1.0°) and scan times (70 s/° and 140 s/°) were compared with a highly redundant data set collected with an Enraf–Nonius CAD4 point detector diffractometer. As part of this analysis it was investigated how the parameters employed during the data reduction performed with theEvalCCDandSORTAVprograms affect the quality of the data. The KappaCCD data sets did not show any significant contamination from λ/2 radiation and possess good internal consistency with lowRintvalues. Decreasing the scan width seems to increase the standard uncertainties, which conversely are improved by an increase in the scan time. The suitability of the KappaCCD instrument to measure data to be used in charge density studies was also examined by performing a charge density data collection with the KappaCCD instrument. The same multipole model was used in the refinement of these data and of the CAD4 data. The two refinements gave almost identical parameters and residual electron densities. The topological analysis of the resulting static electron densities shows that the bond critical points have the same characteristics.
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Sørensen HO, Larsen S. Hydrogen bonding in enantiomeric versus racemic mono-carboxylic acids; a case study of 2-phenoxypropionic acid. Acta Crystallogr B 2003; 59:132-40. [PMID: 12554978 DOI: 10.1107/s0108768102022085] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2002] [Accepted: 11/22/2002] [Indexed: 11/10/2022]
Abstract
The structural and thermodynamic backgrounds for the crystallization behaviour of racemates have been investigated using 2-phenoxypropionic acid (PPA) as an example. The racemate of PPA behaves normally and forms a racemic compound that has a higher melting point and is denser than the enantiomer. Low-temperature crystal structures of the pure enantiomer, the enantiomer cocrystallized with n-alkanes and the racemic acid showed that hydrogen-bonded dimers that form over crystallographic symmetry elements exist in all but the structure of the pure enantiomer. A database search for optically pure chiral mono-carboxylic acids revealed that the hydrogen-bonded cyclic dimer is the most prevalent hydrogen-bond motif in chiral mono-carboxylic acids. The conformation of PPA depends on the hydrogen-bond motif; the antiplanar conformation relative to the ether group is associated with a catemer hydrogen-bonding motif, whereas the more abundant synplanar conformation is found in crystals that contain cyclic dimers. Other intermolecular interactions that involve the substituent of the carboxylic group were identified in the crystals that contain the cyclic dimer. This result shows how important the nature of the substituent is for the crystal packing. The differences in crystal packing have been related to differences in melting enthalpy and entropy between the racemic and enantiomeric acids. In a comparison with the equivalent 2-(4-chlorophenoxy)-propionic acids, the differences between the crystal structures of the chloro and the unsubstituted acid have been identified and related to thermodynamic data.
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Affiliation(s)
- Henning Osholm Sørensen
- Centre for Crystallographic Studies, Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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Bendahl L, Hammershøi A, Jensen DK, Larsen S, Riisager A, Sargeson AM, Sørensen HO. Metal complex amino acid synthons: syntheses, structures and stereoselective reactions of (iminoacetato)cobalt(iii) complexes. ACTA ACUST UNITED AC 2002. [DOI: 10.1039/b202090d] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Mossin S, Sørensen HO, Weihe H. trans-Bis(cyano-kappaC)(1,4,8,11-tetraazacyclotetradecane-kappa4N)manganese(III) perchlorate, a low-spin manganese(III) complex. Acta Crystallogr C 2002; 58:M204-6. [PMID: 11932516 DOI: 10.1107/s0108270102001713] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2002] [Accepted: 01/28/2002] [Indexed: 11/10/2022] Open
Abstract
The crystal structure of the low-spin (S = 1) MnIII complex [Mn(CN)(2)(C(10)H(24)N(4))]ClO(4), or trans-[Mn(CN)(2)(cyclam)](ClO(4)) (cyclam is the tetradentate amine ligand 1,4,8,11-tetraazacyclotetradecane), is reported. The structural parameters in the Mn(cyclam) moiety are found to be insensitive to both the spin and the oxidation state of the Mn ion. The difference between high- and low-spin Mn(III) complexes is that a pronounced tetragonal elongation of the coordination octahedron occurs in high-spin complexes and a slight tetragonal compression is seen in low-spin complexes, as in the title complex.
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Affiliation(s)
- Susanne Mossin
- Inorganic Chemistry, Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100, Denmark.
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Atoh M, Sørensen HO, Andersen P, Hazell RG, Hanfland M, Dooryhee E. Synthesis and Stereochemistry of Cobalt(III) Complexes with the New Optically Active Phosphine Ligand, N,N'-Bis[2-(diphenylphosphanyl)ethyl]-(1R,2R)-cyclohexane-1,2-diamine (ch-PNNP). Crystal Structure of Lambda-Cisbeta-[Co(acac)(ch-PNNP)](ClO4)2. ACTA ACUST UNITED AC 1997. [DOI: 10.3891/acta.chem.scand.51-1169] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Stuhr-Hansen N, Sørensen HO, Henriksen L, Larsen S, Rosendahl CN. Structural Characterisation of Chiral 4-Methoxyphenyl Phenyl Selenoxide. ACTA ACUST UNITED AC 1997. [DOI: 10.3891/acta.chem.scand.51-1186] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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